| RX CC |
| ID: | 1512129706 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 140 (121) | ||
| Sequences: | 140 (128.3) | ||
| Seq/Len: | 1.157 | ||
| Nf(neff/√len): | 11.7 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.157).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 61_V | 113_T | 2.094 | 0.98 |
| 34_L | 48_H | 1.985 | 0.96 |
| 34_L | 64_T | 1.728 | 0.91 |
| 99_A | 112_A | 1.673 | 0.89 |
| 1_M | 41_S | 1.671 | 0.89 |
| 27_F | 65_T | 1.649 | 0.88 |
| 64_T | 109_Q | 1.621 | 0.87 |
| 4_A | 58_I | 1.612 | 0.86 |
| 50_G | 53_I | 1.604 | 0.86 |
| 116_S | 120_L | 1.583 | 0.85 |
| 118_K | 121_K | 1.397 | 0.73 |
| 30_K | 107_V | 1.393 | 0.73 |
| 16_S | 111_M | 1.389 | 0.73 |
| 29_E | 57_E | 1.335 | 0.69 |
| 35_R | 42_C | 1.334 | 0.68 |
| 117_M | 120_L | 1.314 | 0.67 |
| 30_K | 70_D | 1.298 | 0.65 |
| 116_S | 121_K | 1.295 | 0.65 |
| 29_E | 115_D | 1.295 | 0.65 |
| 61_V | 70_D | 1.293 | 0.65 |
| 15_Q | 58_I | 1.291 | 0.65 |
| 117_M | 121_K | 1.285 | 0.64 |
| 11_R | 38_L | 1.279 | 0.64 |
| 26_P | 71_S | 1.276 | 0.63 |
| 52_T | 70_D | 1.264 | 0.62 |
| 44_I | 98_Q | 1.262 | 0.62 |
| 13_I | 17_M | 1.260 | 0.62 |
| 62_A | 120_L | 1.254 | 0.61 |
| 68_M | 106_T | 1.214 | 0.58 |
| 31_L | 66_E | 1.208 | 0.57 |
| 9_L | 70_D | 1.200 | 0.56 |
| 63_Y | 93_F | 1.192 | 0.56 |
| 37_I | 40_K | 1.190 | 0.55 |
| 106_T | 113_T | 1.187 | 0.55 |
| 19_L | 79_A | 1.186 | 0.55 |
| 65_T | 69_V | 1.184 | 0.55 |
| 48_H | 54_L | 1.174 | 0.54 |
| 72_E | 106_T | 1.173 | 0.54 |
| 60_E | 64_T | 1.165 | 0.53 |
| 41_S | 55_E | 1.163 | 0.53 |
| 34_L | 54_L | 1.152 | 0.52 |
| 5_A | 66_E | 1.139 | 0.51 |
| 116_S | 119_D | 1.135 | 0.50 |
| 4_A | 12_T | 1.131 | 0.50 |
| 82_L | 93_F | 1.130 | 0.50 |
| 8_S | 62_A | 1.123 | 0.49 |
| 17_M | 23_D | 1.119 | 0.49 |
| 1_M | 40_K | 1.118 | 0.48 |
| 76_V | 106_T | 1.108 | 0.48 |
| 3_Y | 8_S | 1.102 | 0.47 |
| 38_L | 63_Y | 1.093 | 0.46 |
| 5_A | 103_I | 1.088 | 0.46 |
| 51_L | 61_V | 1.085 | 0.45 |
| 31_L | 99_A | 1.084 | 0.45 |
| 31_L | 97_E | 1.069 | 0.44 |
| 4_A | 9_L | 1.056 | 0.43 |
| 28_Y | 114_S | 1.044 | 0.41 |
| 43_N | 103_I | 1.044 | 0.41 |
| 32_K | 39_E | 1.038 | 0.41 |
| 68_M | 104_D | 1.030 | 0.40 |
| 68_M | 74_R | 1.020 | 0.39 |
| 19_L | 70_D | 1.011 | 0.38 |
| 33_S | 41_S | 1.010 | 0.38 |
| 62_A | 106_T | 1.002 | 0.38 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3qflA | 1 | 0.6714 | 99.6 | 0.589 | Contact Map |
| 4m70A | 5 | 0.7857 | 99.4 | 0.635 | Contact Map |
| 4abxA | 4 | 0.8143 | 15.3 | 0.929 | Contact Map |
| 4xa3A | 2 | 0 | 13.2 | 0.931 | Contact Map |
| 4kxfK | 8 | 0.2857 | 13.1 | 0.931 | Contact Map |
| 1rsoB | 2 | 0.3786 | 8.8 | 0.937 | Contact Map |
| 1nu7D | 2 | 0.7714 | 8.4 | 0.937 | Contact Map |
| 4heoA | 2 | 0.4214 | 8.3 | 0.937 | Contact Map |
| 4n78D | 1 | 0.65 | 7.9 | 0.938 | Contact Map |
| 2a5yB | 2 | 0.7643 | 7.8 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)